Transcript Adding value to open access research data

Adding value to open access
research data:
the eBank UK Project.
Dr Liz Lyon, Director
UKOLN, University of Bath, UK
OAI4, CERN Geneva, October 2005.
UKOLN is supported by:
www.ukoln.ac.uk
a centre of expertise in digital information management
www.bath.ac.uk
Overview
1. e-Research & data-intensive science
2. Repository services & adding value
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Aggregation and linking: eBank UK
Integration and workflows
3. Looking to the longer term: digital
curation and preservation
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1. e-Research & data-intensive science
eScience - the data deluge
Data
Overload!
EPSRC National
Crystallography
Service
How do we
disseminate?
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Diversity of data collections
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Very large, relatively homogeneous:
Large-scale Hadron Collider (LHC) outputs from CERN
Smaller, heterogeneous and richer collections:
World Data Centre for Solar-terrestrial Physics CCLRC
Small-scale laboratory results:
“jumping robots” project at the University of Bath
Population survey data: UK Biobank
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Highly sensitive, personal data: patient care records
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Taxonomy of data collections
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Research collections:
jumping robots
Community collections:
Flybase at Indiana (with
UC Berkeley )
Reference collections:
Protein Data Bank
Evolution……
Source: NSF Long-Lived Digital
Data Collections
Draft report revisedOAI4,
May
2005
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Experience of data-sharing
• Large scale data sharing in the life sciences
Draft Report June 2005
Sponsored by UK research funding bodies
MRC, BBSRC, NERC, JISC, Wellcome
• Outcomes & recommendations
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Importance of standards and good quality metadata
Require a data management plan
Work needed on vocabularies & ontologies
Awareness of archiving & long term preservation
• Position of research funders and policy makers?
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Presentation services: subject, media-specific, data, commercial portals
Data creation /
capture /
gathering:
laboratory
experiments,
Grids,
fieldwork,
surveys, media
Resource
discovery, linking,
embedding
Data analysis,
transformation,
mining, modelling
Searching ,
harvesting,
embedding
Aggregator
services: national,
commercial
Resource
discovery,
linking,
embedding
Learning object
creation, re-use
Harvesting
metadata
Research &
e-Science
workflows
Deposit / selfarchiving
Learning &
Teaching
workflows
Repositories :
institutional,
e-prints, subject,
data, learning objects
Validation
Publication
Resource
discovery, linking,
embedding
The scholarly knowledge cycle.
Liz Lyon, Ariadne, July 2003.
© Liz Lyon (UKOLN, University of Bath), 2005
This work is licensed under a Creative Commons License
Attribution-ShareAlike 2.0
Deposit / selfarchiving
Institutional
presentation
services: portals,
Learning
Management
Systems, u/g, p/g
courses, modules
Peer-reviewed
publications: journals,
conference proceedings
OAI4, CERN Geneva, October 2005
Validation
Quality
assurance
bodies
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Presentation services: subject, media-specific, data, commercial portals
Data creation /
capture /
gathering:
laboratory
experiments,
Grids,
fieldwork,
surveys, media
Resource
discovery, linking,
embedding
Data analysis,
transformation,
mining, modelling
Searching ,
harvesting,
embedding
Aggregator services:
eBank UK
Resource
discovery,
linking,
embedding
Learning object
creation, re-use
Harvesting
metadata
Research &
e-Science
workflows
Deposit / selfarchiving
Learning &
Teaching
workflows
Repositories :
institutional,
e-prints, subject,
data, learning objects
Validation
Publication
Deposit / selfarchiving
Institutional
presentation
services: portals,
Learning
Management
Systems, u/g, p/g
courses, modules
Resource
discovery, linking,
embedding
Peer-reviewed
publications: journals,
conference proceedings
OAI4, CERN Geneva, October 2005
Validation
Quality
assurance
bodies
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2. Repository services & adding
value: the eBank UK Project
eBank UK Project
• Two key themes:
– Open access to datasets
– Linking research data to publications and to learning
• JISC-funded from September 2003: now in Phase 2
• UKOLN at the University of Bath (lead), University of
Southampton, University of Manchester
• Exemplar: e-Science testbed ‘Combechem’
– Grid-enabled combinatorial chemistry / crystallography
– National Crystallography Service
• Resource Discovery Network / PSIgate physical
sciences portal
• http://www.ukoln.ac.uk/projects/ebank-uk/
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The “hybrid” project team
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UKOLN
Michael Day
Monica Duke
Rachel Heery
Traugott Koch
Liz Lyon
+
Andy Powell
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Southampton
Les Carr
Simon Coles
Jeremy Frey
Chris Gutteridge
Mike Hursthouse
Andrew Milstead
• Manchester
• John Blunden-Ellis
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Create
Data Flow in eBank UK
HTML
Deposition
Interface
Submit
Store/link
Institutional
repository
eCrystals
Index
and
Search
Harvest
(XML)
eBank
aggregator
service
Present
HTML
Present
OAI-PMH
Deposit
Service Provider
interfaces e.g.
Subject Portal
Local archive
search
interface
OAI4, CERN Geneva, October 2005
Data files
Metadata
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CombeChem: An EPSRC pilot project
Simulation
Video
Diffractometer
Properties
Analysis
Structures
Database
Properties
e-Lab
X-Ray
e-Lab
Grid Middleware
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Crystallography workflow
RAW DATA
DERIVED DATA
RESULTS DATA
• Initialisation: mount new sample set up data collection
• Collection: collect data
• Processing: process and correct images
• Solution: solve structures
• Refinement: refine structure
• CIF: produce CIF (Crystallographic Information File)
• Validation: chemical & crystallographic checks
• Report: generate Crystal Structure Report
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A data repository entry
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Access to the underlying data:
complex objects
ecrystals.chem.soton.ac.uk
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Harvesting: OAIster
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Aggregating: search & discover
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Linking data to publications
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Embedding in a science portal
for student learners
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Ontologies for discovery in
an inter-disciplinary world
• Transform the ‘list’ into an
‘ontology’
• Embed ontology into the
deposition process
• Aggregators use keywords
for linking with the broader
literature
• Researchers use keyword
ontology in search and
discovery services
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Persistent identifiers for
data citation
• eBank use cases: depositor, author, service
provider, reader, publisher, ?
• Schemes: DOI, Handle, ARK, PURL
• Global identification: express as http URIs
• Added value services: CrossRef, resolution
service, integration (Globus), look-up service, ?
• Degree of trust or persistence
• Costs
• Future potential: political, ?
• Domain identifiers: International Chemical Identifier
(InChI) codes
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Publication & citation of
scientific primary data project
• National Library for Science & Technology (TIB),
University of Hanover, Germany
• STD-DOI Project http://www.std-doi.de
• DOI registry for datasets
• Data requirements: quality control, long-term curation,
use DOI resolver
• Data publication agents: World Data Center Climate,
GeoForschungsZentrum Potsdam
• Exemplar data citation:
– Kamm, H; Machon, L; Donner, S (2004): Gas chromatography
(KTB Field Lab), GFZ Potsdam.
doi:10.1594/GFZ/ICDP/KTB/ktb-geoch-gaschr-p
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Integration into
crystallographic
publishing
practices
Publishers
seal of
approval
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Integration into chemistry
research workflows
• R4L Repository for the Laboratory Project (JISC-funded)
automated data capture from instrumentation, registration of results
• SMART TEA electronic Laboratory notebook + annotations
• Related sub-domains of chemistry: SPECTRa Project (JISC-funded)
• Research assessment (RAE) process?
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Integration into the curriculum
and e-Learning workflows
• MChem course
• Assess role in
Undergraduate
Chemical Informatics
courses
• Pedagogic evaluation
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3. Looking to the longer term:
digital curation & preservation
Repositories and digital curation
For later use?
In use now (and the future)?
Static
Dynamic
Data preservation
Data curation
“maintaining and adding value to a trusted body
of digital information for current and future use”
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Assuring long term access to
the research record
• Trusted digital repositories
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Audit Checklist for Certification Draft Report
Research Libraries Group, August 2005
RLG-NARA Taskforce
Defined criteria under 4 categories
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Organisation
Functions, processes & procedures
Designated community & usability
Technologies & technical infrastructure
• UK Digital Curation Centre http://www.dcc.ac.uk
– 1st International DCC Conference presentations available
– PV2005 Royal Society Edinburgh November 21-23 Nov
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Thank you.
Questions?…..
More information: UKOLN http://www.ukoln.ac.uk/
Dataset
Searching,
linking and
embedding
eBank data model
Dataset
Dataset
dcterms:references
Harvesting
OAI-PMH
oai_dc
Crystal structure
(data holding)
Linking
ebank_dc
record (XML)
dc:identifier
dc:type=“CrystalStructure”
and/or “Collection”
Institutional
repository
Crystal structure
report (HTML)
Searching,
linking and
embedding
Harvesting
OAI-PMH
PSIgate
portal
ebank_dc
eBank UK
aggregator
service
dcterms:isReferencedBy
Eprint
“jump-off”
page
(HTML)
Eprint
manifestation
(e.g. PDF)
Deposit
ePrint UK
aggregator
service
dc:identifier
Linking
Model input Andy Powell, UKOLN.
Harvesting
OAI-PMH
oai_dc
Eprint oai_dc
record (XML)
dc:type=“Eprint”
and/or ”Text”
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Subject service
Searching,
linking and
embedding
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